Biological optical analysis instruments, such as genetic sequencers, tend to include multiple configurable components, each with multiple degrees of freedom. Increasing complexity of these biological optical analysis instruments has led to increased manufacturing and operation expense. Generally, these types of instruments benefit from precise alignment of their many internal optical components. In some genetic sequencing instruments, for example, internal components are generally aligned within precise tolerances. Many manufacturing techniques for such instruments involve installing all of the components on a precision plate, and then configuring and aligning each component. Component alignment may change during shipping or use. For example, temperature changes may alter alignments. Re-aligning each component takes time and skill. In some examples, there may be over 30 total degrees of freedom available across all of the components and they interact to each other. The large number of degrees of freedom complicates alignment and configuration and adds time and expense to system operation. Optical sequencer fabrication and operation may be simplified by reducing the degrees of freedom available across all system components through a modular architecture.
Optical sequencers may use laser line illumination to detect and sequence a biological specimen. For example, laser line illumination may enable high throughput scanning using a time delay integration (TDI) sensor to detect fluorescence emissions from a sample flowcell. The detected emissions may be used to identify and sequence genetic components of the biological sample. However, at high scanning speeds and/or laser output powers, functionality may be impacted by photo-saturation of the fluorophores and/or photo-bleaching of the fluorophores, and/or photo-induced damage to the sample. High power lasers can also cause damage to the objective lens, including the bonding adhesive, coatings and glass.